X-114583809-G-A

Variant names:

• chrX-114583809-G-A
• rs3813928

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.128 in 107,870 control chromosomes in the GnomAD database, including 756 homozygotes. There are 4,030 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.13 (756 hom., 4030 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0260
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant X-114583809-G-A is Benign according to our data. Variant chrX-114583809-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1318441.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 13832 AN: 107817 Hom.: 757 Cov.: 21

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0311

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.129

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.128 AC: 13836 AN: 107870 Hom.: 756 Cov.: 21 AF XY: 0.132 AC XY: 4030 AN XY: 30538

African (AFR) AF: 0.0299 AC: 886 AN: 29602

American (AMR) AF: 0.143 AC: 1450 AN: 10128

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 383 AN: 2595

East Asian (EAS) AF: 0.132 AC: 443 AN: 3353

South Asian (SAS) AF: 0.278 AC: 667 AN: 2397

European-Finnish (FIN) AF: 0.156 AC: 856 AN: 5483

Middle Eastern (MID) AF: 0.115 AC: 24 AN: 209

European-Non Finnish (NFE) AF: 0.172 AC: 8918 AN: 51967

Other (OTH) AF: 0.129 AC: 188 AN: 1460

Alfa AF: 0.140 Hom.: 5946

Bravo AF: 0.119

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 14, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 15741483, 16021472)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		-0.026
PromoterAI		0.031	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3813928; hg19: chrX-113818282;